Align D-lactate transporter, permease component 2 (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__psRCH2:GFF3786 Length = 295 Score = 176 bits (447), Expect = 5e-49 Identities = 113/335 (33%), Positives = 166/335 (49%), Gaps = 51/335 (15%) Query: 1 MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60 + A L Q+L GL GS YA+++LGL +IFG L ++NFAHGA +MIGAF + L + Sbjct: 9 IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATLGIG 68 Query: 61 FETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGV-GYVME 119 + W L PI++G+ V+E Sbjct: 69 Y------------------------------------WPA----LILAPIIVGLCSAVIE 88 Query: 120 RGLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMD 179 R + Y H +L TFGLA+ L+ +YFYG++ P L G NLG + Sbjct: 89 RLALSRLYNLDHLYSLLFTFGLALALEGAFRYFYGSSGQPYAVPKELAGGYNLGFMF--- 145 Query: 180 IVYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFG 239 P +R ++VI + ++ T G +RA + V GIN+ T +G Sbjct: 146 --LPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAATENPTLVRTFGINVPLLLTFTYG 203 Query: 240 IAAAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFA 299 + AA+AGLAG++ PI + MG + +++ F VVVVGGMGS+ GA++ G++LG+LE Sbjct: 204 MGAALAGLAGMLAAPIYQVSPLMGSNLIIVVFAVVVVGGMGSILGAIITGYMLGILEGLT 263 Query: 300 SMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGR 334 K P I+I+V+ I+LL RP GLMGR Sbjct: 264 -----KVFYPEASNIVIFVIMAIVLLVRPAGLMGR 293 Lambda K H 0.329 0.147 0.439 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 272 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 295 Length adjustment: 27 Effective length of query: 313 Effective length of database: 268 Effective search space: 83884 Effective search space used: 83884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory